Started by user administrator Building in workspace /var/lib/jenkins/jobs/API Documentation - trunk/workspace Updating https://repository.dataone.org/documents/Projects/cicore/architecture/api-documentation at revision '2017-03-27T17:03:37.906 +0000' A source/design/UseCases/uml A source/design/UseCases/uml/01_seq.uml A source/design/UseCases/uml/images AU source/design/UseCases/uml/images/01_seq.png A source/design/UseCases/uml/05_seq.uml Fetching 'https://repository.dataone.org/software/cicore/tags/D1_SCHEMA_1_0_2' at -1 into '/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/D1_SCHEMA_v1' At revision 18747 Fetching 'https://repository.dataone.org/software/cicore/branches/D1_SCHEMA_v1.1' at -1 into '/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/D1_SCHEMA_v1.1' At revision 18747 Fetching 'https://repository.dataone.org/software/cicore/trunk/d1_schemas' at -1 into '/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/D1_SCHEMA_DEV' At revision 18747 Fetching 'https://repository.dataone.org/software/tools/trunk/docutils' at -1 into '/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/docutils' At revision 18747 Fetching 'https://repository.dataone.org/software/tools/trunk/xsd2rst' at -1 into '/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/xsd2rst' At revision 18747 At revision 18747 No changes for https://repository.dataone.org/software/cicore/tags/D1_SCHEMA_1_0_2 since the previous build No changes for https://repository.dataone.org/software/cicore/branches/D1_SCHEMA_v1.1 since the previous build No changes for https://repository.dataone.org/software/cicore/trunk/d1_schemas since the previous build No changes for https://repository.dataone.org/software/tools/trunk/docutils since the previous build No changes for https://repository.dataone.org/software/tools/trunk/xsd2rst since the previous build [workspace] $ /bin/sh -xe /tmp/hudson8292220148807472809.sh + cd /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation + export PATH=/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/local/bin + export GRAPHVIZ=/usr/bin/dot + pwd /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation + echo /usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/local/bin /usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/local/bin + echo === === + which java + echo /usr/lib/jvm/java-7-openjdk-amd64/bin/java /usr/lib/jvm/java-7-openjdk-amd64/bin/java + java -version java version "1.7.0_121" OpenJDK Runtime Environment (IcedTea 2.6.8) (7u121-2.6.8-1ubuntu0.12.04.3) OpenJDK 64-Bit Server VM (build 24.121-b00, mixed mode) + echo + make clean rm -rf "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/build" + make all /usr/bin/xsltproc --path ".:source/D1_SCHEMA_DEV:tools/xsd2rst" dataoneTypes2rst.xsl source/D1_SCHEMA_DEV/dataoneTypes.xsd > "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/apis/Types.txt" /usr/bin/xsltproc --path ".:source/D1_SCHEMA_DEV:tools/xsd2rst" dataoneTypes2rst.xsl source/D1_SCHEMA_DEV/dataoneTypes_v1.1.xsd > "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/apis/Types11.txt" /usr/bin/xsltproc --path ".:source/D1_SCHEMA_DEV:tools/xsd2rst" dataoneTypes2rst.xsl source/D1_SCHEMA_DEV/dataoneTypes_v2.0.xsd > "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/apis/Types2.txt" /usr/bin/python "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/ihwd/ihwd.py" -s "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/MethodCrossReference.xls" -d "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/apis/generated" INFO:root:Processing /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/MethodCrossReference.xls INFO:root:Generating exception list INFO:generateRESTSummaryTable:Order: [u'MNCore', u'MNRead', u'MNAuthorization', u'MNStorage', u'MNReplication', u'MNQuery', u'MNView', u'MNPackage', u'CNCore', u'CNRead', u'CNAuthorization', u'CNIdentity', u'CNReplication', u'CNRegister', u'CNView', u'CNDiagnostic'] INFO:generateRESTSummaryTable:Module: MNCore INFO:generateRESTSummaryTable:Function: ping INFO:generateRESTSummaryTable:Function: getLogRecords INFO:generateRESTSummaryTable:Function: getCapabilities INFO:generateRESTSummaryTable:Module: MNRead INFO:generateRESTSummaryTable:Function: get INFO:generateRESTSummaryTable:Function: getSystemMetadata INFO:generateRESTSummaryTable:Function: describe INFO:generateRESTSummaryTable:Function: getChecksum INFO:generateRESTSummaryTable:Function: listObjects INFO:generateRESTSummaryTable:Function: synchronizationFailed INFO:generateRESTSummaryTable:Function: systemMetadataChanged INFO:generateRESTSummaryTable:Function: getReplica INFO:generateRESTSummaryTable:Module: MNAuthorization INFO:generateRESTSummaryTable:Function: isAuthorized INFO:generateRESTSummaryTable:Module: MNStorage INFO:generateRESTSummaryTable:Function: create INFO:generateRESTSummaryTable:Function: update INFO:generateRESTSummaryTable:Function: generateIdentifier INFO:generateRESTSummaryTable:Function: delete INFO:generateRESTSummaryTable:Function: archive INFO:generateRESTSummaryTable:Function: updateSystemMetadata INFO:generateRESTSummaryTable:Module: MNReplication INFO:generateRESTSummaryTable:Function: replicate INFO:generateRESTSummaryTable:Module: MNQuery INFO:generateRESTSummaryTable:Function: query INFO:generateRESTSummaryTable:Function: getQueryEngineDescription INFO:generateRESTSummaryTable:Function: listQueryEngines INFO:generateRESTSummaryTable:Module: MNView INFO:generateRESTSummaryTable:Function: view INFO:generateRESTSummaryTable:Function: listViews INFO:generateRESTSummaryTable:Module: MNPackage INFO:generateRESTSummaryTable:Function: getPackage INFO:generateRESTSummaryTable:Module: CNCore INFO:generateRESTSummaryTable:Function: ping INFO:generateRESTSummaryTable:Function: create INFO:generateRESTSummaryTable:Function: listFormats INFO:generateRESTSummaryTable:Function: getFormat INFO:generateRESTSummaryTable:Function: getLogRecords INFO:generateRESTSummaryTable:Function: reserveIdentifier INFO:generateRESTSummaryTable:Function: generateIdentifier INFO:generateRESTSummaryTable:Function: listChecksumAlgorithms INFO:generateRESTSummaryTable:Function: setObsoletedBy INFO:generateRESTSummaryTable:Function: delete INFO:generateRESTSummaryTable:Function: archive INFO:generateRESTSummaryTable:Function: listNodes INFO:generateRESTSummaryTable:Function: getCapabilities INFO:generateRESTSummaryTable:Function: registerSystemMetadata INFO:generateRESTSummaryTable:Function: updateSystemMetadata INFO:generateRESTSummaryTable:Function: hasReservation INFO:generateRESTSummaryTable:Module: CNRead INFO:generateRESTSummaryTable:Function: get INFO:generateRESTSummaryTable:Function: getSystemMetadata INFO:generateRESTSummaryTable:Function: describe INFO:generateRESTSummaryTable:Function: resolve INFO:generateRESTSummaryTable:Function: getChecksum INFO:generateRESTSummaryTable:Function: listObjects INFO:generateRESTSummaryTable:Function: search INFO:generateRESTSummaryTable:Function: query INFO:generateRESTSummaryTable:Function: getQueryEngineDescription INFO:generateRESTSummaryTable:Function: listQueryEngines INFO:generateRESTSummaryTable:Function: synchronize INFO:generateRESTSummaryTable:Module: CNAuthorization INFO:generateRESTSummaryTable:Function: setRightsHolder INFO:generateRESTSummaryTable:Function: isAuthorized INFO:generateRESTSummaryTable:Function: setAccessPolicy INFO:generateRESTSummaryTable:Module: CNIdentity INFO:generateRESTSummaryTable:Function: registerAccount INFO:generateRESTSummaryTable:Function: updateAccount INFO:generateRESTSummaryTable:Function: verifyAccount INFO:generateRESTSummaryTable:Function: getSubjectInfo INFO:generateRESTSummaryTable:Function: listSubjects INFO:generateRESTSummaryTable:Function: mapIdentity INFO:generateRESTSummaryTable:Function: removeMapIdentity INFO:generateRESTSummaryTable:Function: requestMapIdentity INFO:generateRESTSummaryTable:Function: confirmMapIdentity INFO:generateRESTSummaryTable:Function: getPendingMapIdentity INFO:generateRESTSummaryTable:Function: denyMapIdentity INFO:generateRESTSummaryTable:Function: createGroup INFO:generateRESTSummaryTable:Function: updateGroup INFO:generateRESTSummaryTable:Module: CNReplication INFO:generateRESTSummaryTable:Function: setReplicationStatus INFO:generateRESTSummaryTable:Function: updateReplicationMetadata INFO:generateRESTSummaryTable:Function: setReplicationPolicy INFO:generateRESTSummaryTable:Function: isNodeAuthorized INFO:generateRESTSummaryTable:Function: deleteReplicationMetadata INFO:generateRESTSummaryTable:Module: CNRegister INFO:generateRESTSummaryTable:Function: updateNodeCapabilities INFO:generateRESTSummaryTable:Function: getNodeCapabilities INFO:generateRESTSummaryTable:Function: register INFO:generateRESTSummaryTable:Module: CNView INFO:generateRESTSummaryTable:Function: view INFO:generateRESTSummaryTable:Function: listViews INFO:generateRESTSummaryTable:Module: CNDiagnostic INFO:generateRESTSummaryTable:Function: echoCredentials INFO:generateRESTSummaryTable:Function: echoSystemMetadata INFO:generateRESTSummaryTable:Function: echoIndexedObject INFO:root:Generating module MNStorage INFO:root:Generating module MNQuery INFO:root:Generating module CNView INFO:root:Generating module CNDiagnostic INFO:root:Generating module CNCore INFO:root:Generating module CNIdentity INFO:root:Generating module CNRead INFO:root:Generating module MNRead INFO:root:Generating module MNReplication INFO:root:Generating module CNAuthorization INFO:root:Generating module MNCore INFO:root:Generating module MNPackage INFO:root:Generating module MNAuthorization INFO:root:Generating module MNView INFO:root:Generating module CNRegister INFO:root:Generating module CNReplication INFO:root:Generating module module_summary INFO:root:Module summary doc MN_function_table INFO:root:Module summary doc CN_function_table INFO:root:Done. GRAPHVIZ_DOT=/usr/bin/dot /usr/bin/java -jar "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/docutils/plantuml.jar" "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source" "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design" GRAPHVIZ_DOT=/usr/bin/dot /usr/bin/java -jar "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/docutils/plantuml.jar" "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/UseCases/uml/*.uml" GRAPHVIZ_DOT=/usr/bin/dot /usr/bin/java -jar "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/docutils/plantuml.jar" "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/apis" GRAPHVIZ_DOT=/usr/bin/dot /usr/bin/java -jar "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/tools/docutils/plantuml.jar" "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/morpho" sphinx-build -b html -d "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/build/doctrees" source "/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/build/html" Running Sphinx v1.5.2 making output directory... /usr/local/lib/python2.7/dist-packages/sphinx/util/requests.py:38: UserWarning: Some links may return broken results due to being unable to check the Server Name Indication (SNI) in the returned SSL cert against the hostname in the url requested. Recommended to install "requests[security]" as a dependency or upgrade to a python version with SNI support (Python 3 and Python 2.7.9+). 'Some links may return broken results due to being unable to ' loading pickled environment... not yet created WARNING: latex_preamble is deprecated. Use latex_elements['preamble'] instead. building [mo]: targets for 0 po files that are out of date building [html]: targets for 134 source files that are out of date updating environment: 134 added, 0 changed, 0 removed reading sources... [ 0%] about reading sources... [ 1%] acknowledgements reading sources... [ 2%] apis/CN_APIs reading sources... [ 2%] apis/CN_internal_APIs reading sources... [ 3%] apis/Exceptions reading sources... [ 4%] apis/ITK_APIs reading sources... [ 5%] apis/MN_APIs reading sources... [ 5%] apis/Types reading sources... [ 6%] apis/Types11 reading sources... [ 7%] apis/Types2 reading sources... [ 8%] apis/index reading sources... [ 8%] apis/monitoring reading sources... 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[ 68%] design/geohash reading sources... [ 69%] design/index reading sources... [ 70%] design/itk-analysis reading sources... [ 70%] design/itk-d1r reading sources... [ 71%] design/itk-java-lib reading sources... [ 72%] design/itk-kepler reading sources... [ 73%] design/itk-libraries reading sources... [ 73%] design/itk-matlab reading sources... [ 74%] design/itk-metadata reading sources... [ 75%] design/itk-overview reading sources... [ 76%] design/itk-python-lib reading sources... [ 76%] design/itk-vistrails reading sources... [ 77%] design/itk-web reading sources... [ 78%] design/logging reading sources... [ 79%] design/querying_content reading sources... [ 79%] design/search_auth reading sources... [ 80%] design/security-plan reading sources... [ 81%] design/usecases reading sources... [ 82%] design/userscenarios reading sources... [ 82%] design/what_is_it reading sources... [ 83%] glossary reading sources... [ 84%] implementation/components reading sources... 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[100%] todo /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:582: ERROR: Unexpected indentation. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:674: WARNING: Bullet list ends without a blank line; unexpected unindent. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:682: WARNING: Bullet list ends without a blank line; unexpected unindent. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:689: WARNING: Bullet list ends without a blank line; unexpected unindent. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:121: ERROR: Unknown target name: "rfc4510". /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authentication.txt:640: ERROR: Unknown target name: "tokens". /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/Authorization.txt:418: WARNING: Include file u'/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/d1_schemas/accesspolicy-example.xml' not found or reading it failed /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt:609: WARNING: duplicate label of equation c16, other instance in /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt:635: WARNING: duplicate label of equation c17, other instance in /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt:918: ERROR: Unexpected indentation. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ContentMutability.txt:1188: SEVERE: Title level inconsistent: Prioritized goals ^^^^^^^^^^^^^^^^^ /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/DataPackage.txt:378: WARNING: nonlocal image URI found: http://www.openarchives.org/ore/1.0/datamodel-images/ore_uml.png /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ExternalContent.txt:109: ERROR: Content block expected for the "TODO" directive; none found. /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ExternalContent.txt:82: ERROR: Unknown target name: "search ui". /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/ExternalContent.txt:116: ERROR: Unknown target name: "index documentation". /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/LoggingSchema.txt:185: WARNING: Include file u'/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/d1_schemas/log_instance_example.xml' not found or reading it failed /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/LoggingSchema.txt:194: WARNING: Include file u'/var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/d1_schemas/logging.xsd' not found or reading it failed /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/NodeIdentity.txt:129: WARNING: undecodable source characters, replacing with "?": ' as per that node>>>\xd5<<". /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/glossary.txt:171: ERROR: Unknown target name: "iana media type". looking for now-outdated files... none found pickling environment... done checking consistency... /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/design/d1_cn_os_core_configuration.txt:: WARNING: document isn't included in any toctree /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/notes/sysmeta_mutation_20101217.txt:: WARNING: document isn't included in any toctree /var/lib/jenkins/jobs/API Documentation - trunk/workspace/api-documentation/source/todo.txt:: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] about writing output... [ 1%] acknowledgements writing output... [ 2%] apis/CN_APIs writing output... [ 2%] apis/CN_internal_APIs writing output... [ 3%] apis/Exceptions writing output... [ 4%] apis/ITK_APIs writing output... [ 5%] apis/MN_APIs writing output... [ 5%] apis/Types writing output... [ 6%] apis/Types11 writing output... [ 7%] apis/Types2 writing output... [ 8%] apis/index writing output... [ 8%] apis/monitoring writing output... [ 9%] apis/rest_comms writing output... [ 10%] changelog writing output... [ 11%] design/Authentication writing output... [ 11%] design/AuthnAndAuthzRequirements writing output... [ 12%] design/Authorization writing output... [ 13%] design/Authorization-technologies writing output... [ 14%] design/AuthorizationAndAuthentication writing output... [ 14%] design/CitationManagerSupport writing output... [ 15%] design/ContentImmutability writing output... [ 16%] design/ContentMutability writing output... 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